Fig. 5: Condensin depletion sharpens A/B compartmentalization while preserving microcompartments.

a, Overview of the experimental system. As previously described¹⁷, G1E-ER4 cells with mCherry-tagged SMC2–mAID are PM-arrested using nocodazole and treated with auxin to induce rapid depletion of SMC2 for 0, 0.5, 1, 4 and 8 h at the end of an 8-h (all but the 8-h depletion) or 15-h (the 8-h depletion) nocodazole arrest. SMC2 degradation eliminates both condensins I and II. Cells are then RCMC-crosslinked, sorted for M-phase purity and processed into sequencing libraries using the RCMC protocol. b, RCMC contact maps comparing the Klf1 (plus zoomed-in boxes), Dag1, Id1 and Cdt1 loci following 0, 1 and 4 h of SMC2 degradation. Interaction annotations generated from the M-to-G1 RCMC data are overlaid below the diagonal. Right, contact intensity scaling. c, Plots of individual loop strengths in the 1-h (top) and 4-h (bottom) depletion conditions, plotted against the strengths in the control 0-h depletion condition (x axes), for P–P loops (left) and CTCF/RAD21–CTCF/RAD21 loops (right). Loops were defined by their exclusive identities (no CRE and CTCF overlap) and strengths were calculated as the observed over expected signal. d, APA plots of called interactions, separated to show exclusively defined P–P, E–P, E–E, E/P–CTCF and CTCF–CTCF loops across SMC2 depletion. Plots show a 20-kb window centered on the loop at 500-bp resolution. e, Compartmentalization signature for the 4-h SMC2 depletion condition at the Dag1 locus. Eigenvector decomposition of interaction frequencies is shown above the contact map, with transition states between positive and negative values noted as black lines overlaid atop the RCMC map. The 4-h depletion condition is shown above the diagonal while the control 0-h depletion is shown below the diagonal. Of the 363 annotated microcompartment anchors across all target loci, 220 (61%) lie within A compartments and 39% lie within B compartments. Of the 3,350 annotated microcompartment loops, 1,941 (58%) are intra-A interactions, 803 (24%) are intra-B interactions and 606 (18%) are inter-A/B interactions. f, Saddle plots of progressive compartmentalization across the 0-h, 1-h and 4-h depletion conditions at the Klf1, Dag1, Id1 and Cdt1 loci. Track showing the strengths of the two compartments and their transition point, in which B-compartmental regions (for example, low eigenvector values) are shown toward the bottom and left of the track while A-compartmental regions (for example, high eigenvector values) are shown on the top and right. Each track is ordered by the eigenvector component values for the specified locus in the indicated treatment condition. g, Interaction probability curves comparing the interaction frequency at different genomic separations (s) for the five condensin depletion datasets. The first derivative of these P(s) curves is shown at the bottom.